[English] 日本語
Yorodumi
- EMDB-64611: Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) boun... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64611
TitleCryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and beta-arrestin 1 (Conformation 2)
Map dataMain map
Sample
  • Complex: G protein-coupled receptor 1 in complex with chemerin and beta-arrestin1
    • Protein or peptide: Retinoic acid receptor responder protein 2
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: Nanobody 32
    • Protein or peptide: Chemerin-like receptor 2,Vasopressin V2 receptor
    • Protein or peptide: Single-chain fragment variable 30 (scFv30)
KeywordsG protein-coupled receptor 1 / chemerin / beta-arrestin1 / signaling protein / MEMBRANE PROTEIN/IMMUNE SYSTEM / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


adipokinetic hormone binding / adipokinetic hormone receptor activity / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / platelet dense granule lumen / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / regulation of lipid catabolic process / antifungal innate immune response ...adipokinetic hormone binding / adipokinetic hormone receptor activity / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / platelet dense granule lumen / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / regulation of lipid catabolic process / antifungal innate immune response / angiotensin receptor binding / hemostasis / TGFBR3 regulates TGF-beta signaling / Activation of SMO / telencephalon development / embryonic digestive tract development / antifungal humoral response / response to caloric restriction / negative regulation of interleukin-8 production / positive regulation of chemotaxis / G protein-coupled receptor internalization / arrestin family protein binding / neuropeptide binding / Lysosome Vesicle Biogenesis / negative regulation of NF-kappaB transcription factor activity / positive regulation of cardiac muscle hypertrophy / stress fiber assembly / Golgi Associated Vesicle Biogenesis / positive regulation of macrophage chemotaxis / positive regulation of vasoconstriction / positive regulation of Rho protein signal transduction / pseudopodium / positive regulation of systemic arterial blood pressure / negative regulation of interleukin-6 production / positive regulation of intracellular signal transduction / positive regulation of receptor internalization / endocytic vesicle / negative regulation of Notch signaling pathway / enzyme inhibitor activity / neuropeptide signaling pathway / positive regulation of fat cell differentiation / retinoid metabolic process / activation of adenylate cyclase activity / cellular response to hormone stimulus / insulin-like growth factor receptor binding / clathrin-coated pit / response to cytokine / negative regulation of protein ubiquitination / extracellular matrix / GTPase activator activity / cytoplasmic vesicle membrane / Activated NOTCH1 Transmits Signal to the Nucleus / response to activity / clathrin-coated endocytic vesicle membrane / Signaling by high-kinase activity BRAF mutants / G protein-coupled receptor binding / G protein-coupled receptor activity / MAP2K and MAPK activation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of protein phosphorylation / chemotaxis / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / endocytic vesicle membrane / Vasopressin regulates renal water homeostasis via Aquaporins / Signaling by BRAF and RAF1 fusions / insulin receptor signaling pathway / Platelet degranulation / Cargo recognition for clathrin-mediated endocytosis / glucose homeostasis / protein transport / Clathrin-mediated endocytosis / : / Thrombin signalling through proteinase activated receptors (PARs) / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / defense response to Gram-negative bacterium / G alpha (s) signalling events / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / neuron projection / endosome / defense response to Gram-positive bacterium / Ub-specific processing proteases / protein ubiquitination / nuclear body / G protein-coupled receptor signaling pathway / inflammatory response / signaling receptor binding / Golgi membrane / negative regulation of cell population proliferation / lysosomal membrane / innate immune response / intracellular membrane-bounded organelle / positive regulation of cell population proliferation
Similarity search - Function
Chemerin-like receptor 2 / Retinoic acid receptor responder protein 2 / Vasopressin V2 receptor / Vasopressin receptor / Formyl peptide receptor-related / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal ...Chemerin-like receptor 2 / Retinoic acid receptor responder protein 2 / Vasopressin V2 receptor / Vasopressin receptor / Formyl peptide receptor-related / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / Cystatin superfamily / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Immunoglobulin E-set
Similarity search - Domain/homology
Vasopressin V2 receptor / Chemerin-like receptor 2 / Beta-arrestin-1 / Retinoic acid receptor responder protein 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Escherichia phage EcSzw-2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCai H / Lin X / Zhao L / He M / Yu J / Zhang B / Ma Y / Xie C / Shui W / Zhao Q ...Cai H / Lin X / Zhao L / He M / Yu J / Zhang B / Ma Y / Xie C / Shui W / Zhao Q / Zhu Y / Wu B
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82121005 China
National Natural Science Foundation of China (NSFC)32401012 China
CitationJournal: Science / Year: 2025
Title: Noncanonical agonist-dependent and -independent arrestin recruitment of GPR1
Authors: Cai H / Lin X / Zhao L / He M / Yu J / Zhang B / Ma Y / Chang X / Tang Y / Luo T / Jiang J / Ma M / Song W / Ma L / Chu X / Yi C / Chen K / Han S / Xie C / Shui W / Zhao Q / Zhu Y / Wu B
History
DepositionMay 15, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_64611.png

Downloads & links

-
Map

FileDownload / File: emd_64611.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.176 Å		1.07 Å/pix.
x 256 pix.
= 274.176 Å		1.07 Å/pix.
x 256 pix.
= 274.176 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.1147239 - 1.7983449
Average (Standard dev.)-0.00019867969 (±0.03537244)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.176 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map

Fileemd_64611_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map

Fileemd_64611_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : G protein-coupled receptor 1 in complex with chemerin and beta-ar...

EntireName: G protein-coupled receptor 1 in complex with chemerin and beta-arrestin1
Components
  • Complex: G protein-coupled receptor 1 in complex with chemerin and beta-arrestin1
    • Protein or peptide: Retinoic acid receptor responder protein 2
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: Nanobody 32
    • Protein or peptide: Chemerin-like receptor 2,Vasopressin V2 receptor
    • Protein or peptide: Single-chain fragment variable 30 (scFv30)

-
Supramolecule #1: G protein-coupled receptor 1 in complex with chemerin and beta-ar...

SupramoleculeName: G protein-coupled receptor 1 in complex with chemerin and beta-arrestin1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Retinoic acid receptor responder protein 2

MacromoleculeName: Retinoic acid receptor responder protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.720475 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MKTIIALSYI FCLVFAELTE AQRRGLQVAL EEFHKHPPVQ WAFQETSVES AVDTPFPAGI FVRLEFKLQQ TSCRKRDWKK PECKVRPNG RKRKCLACIK LGSEDKVLGR LVHCPIETQV LREAEEHQET QCLRVQRAGE DPHSFYFPGQ FAFS

UniProtKB: Retinoic acid receptor responder protein 2

-
Macromolecule #2: Beta-arrestin-1

MacromoleculeName: Beta-arrestin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.167137 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTAA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPSSVTL QPGPEDTGKA IGVDYEVKAF VAENLEEKIH K RNSVRLVI ...String:
MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTAA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPSSVTL QPGPEDTGKA IGVDYEVKAF VAENLEEKIH K RNSVRLVI EKVQYAPERP GPQPTAETTR QFLMSDKPLH LEASLDKEIY YHGEPISVNV HVTNNTNKTV KKIKISVRQY AD IVLFNTA QYKVPVAMEE ADDTVAPSST FSKVYTLTPF LANNREKRGL ALDGKLKHED TNLASSTLLR EGANREILGI IVS YKVKVK LVVSRGGLLG DLASSDVAVE LPFTLMHPKP KEEPPHREVP ENETPVDTNL

UniProtKB: Beta-arrestin-1

-
Macromolecule #3: Nanobody 32

MacromoleculeName: Nanobody 32 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage EcSzw-2 (virus)
Molecular weightTheoretical: 13.238716 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCVVSGFFFD TVTMAWYRRA PGKHRELVAS ATAGGTTTYA DSVKDRFTIS RDNAKNTVYL QMNSLKPED TAVYYCNTFV RSLSWGQGTQ VTVSSHHHHH H

-
Macromolecule #4: Chemerin-like receptor 2,Vasopressin V2 receptor

MacromoleculeName: Chemerin-like receptor 2,Vasopressin V2 receptor / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.071438 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: WSHPQFEKGS GAGASAGSWS HPQFEKGSDY KDDDDKEFLE VLFQGPEDLE ETLFEEFENY SYDLDYYSLE SDLEEKVQLG VVHWVSLVL YCLAFVLGIP GNAIVIWFTG FKWKKTVTTL WFLNLAIADF IFLLFLPLYI SYVAMNFHWP FGIWLCKANS F TAQLNMFA ...String:
WSHPQFEKGS GAGASAGSWS HPQFEKGSDY KDDDDKEFLE VLFQGPEDLE ETLFEEFENY SYDLDYYSLE SDLEEKVQLG VVHWVSLVL YCLAFVLGIP GNAIVIWFTG FKWKKTVTTL WFLNLAIADF IFLLFLPLYI SYVAMNFHWP FGIWLCKANS F TAQLNMFA SVFFLTVISL DHYIHLIHPV LSHRHRTLKN SLIVIIFIWL LASLIGGPAL YFRDTVEFNN HTLCYNNFQK HD PDLTLIR HHVLTWVKFI IGYLFPLLTM SICYLCLIFK VKKRSILISS RHFWTILVVV VAFVVCWTPY HLFSIWELTI HHN SYSHHV MQAGIPLSTG LAFLNSCLNP ILYVLISKKF QARFRSSVAE IARGRTPPSL GPQDE(SEP)C(TPO)(TPO)A (SEP)(SEP)(SEP)LAKDTS S

UniProtKB: Chemerin-like receptor 2, Vasopressin V2 receptor

-
Macromolecule #5: Single-chain fragment variable 30 (scFv30)

MacromoleculeName: Single-chain fragment variable 30 (scFv30) / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.157861 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKG TTAASGSSGG SSSGAEVQLV ESGGGLVQPG GSLRLSCAAS GFNVYSSSIH W VRQAPGKG ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKG TTAASGSSGG SSSGAEVQLV ESGGGLVQPG GSLRLSCAAS GFNVYSSSIH W VRQAPGKG LEWVASISSY YGYTYYADSV KGRFTISADT SKNTAYLQMN SLRAEDTAVY YCARSRQFWY SGLDYWGQGT LV TVSSA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.1875 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112084
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more